cellsamsegmentation-pluripotent-differentiation

Perform CellSAM segmentation interactively

https://github.com/deepshika96/cellsamsegmentation-pluripotent-differentiation

Science Score: 57.0%

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Repository

Perform CellSAM segmentation interactively

Basic Info

Host: GitHub
Owner: deepshika96
License: mit
Default Branch: main
Homepage:
Size: 11.7 KB

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Created 9 months ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

PhD

🧠 Interactive Cell Segmentation with CellSAM

This repository provides an interactive pipeline for threshold-based preprocessing and segmentation of biological images using the CellSAM deep learning framework. The workflow includes image cropping, brightness adjustment, interactive thresholding, segmentation, and exporting results as TIFF masks and Excel summaries.

📂 Features

Crop and preprocess PNG images
Stretch image contrast dynamically
Interactive threshold slider using ipywidgets
Deep learning segmentation with CellSAM
Object counting using connected component labeling
Export results as .tif masks and Excel .xlsx summary

CellSAM:

@article{israel2023foundation, title={A Foundation Model for Cell Segmentation}, author={Israel, Uriah and Marks, Markus and Dilip, Rohit and Li, Qilin and Schwartz, Morgan and Pradhan, Elora and Pao, Edward and Li, Shenyi and Pearson-Goulart, Alexander and Perona, Pietro and others}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory Preprints}, doi = {10.1101/2023.11.17.567630}, }

📦 Requirements

Install the required packages:

```bash pip install -r requirements.txt

Owner

Login: deepshika96
Kind: user

Repositories: 2
Profile: https://github.com/deepshika96

Citation (citation.cff)

cff-version: 1.2.0
title: CellSAM-pluripotent
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Deepshika
    family-names: Arasu
    email: deepshika96@gmail.com
    affiliation: University Of Barcelona
identifiers:
  - type: url
    value: 'https://github.com/deepshika96/CellSAMsegmentation-pluripotent-differentiation'
abstract: >-
  Performs CellSAM segemention on 2D images-
  with inbuilt interactive image analysis.
license: MIT-0

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Dependencies

requirements.txt pypi

imageio *
ipywidgets *
matplotlib *
numpy *
pandas *
scikit-image *
tifffile *

ecosyste.ms

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